def test_kpoint_algebra(self):
"""Test k-point algebra."""
lattice = self.lattice
gamma = Kpoint([0, 0, 0], lattice)
pgamma = Kpoint([1, 0, 1], lattice)
X = Kpoint([0.5, 0, 0], lattice)
K = Kpoint([1/3, 1/3, 1/3], lattice)
print(X)
self.serialize_with_pickle(X, protocols=[-1])
self.assert_almost_equal(X.versor().norm, 1.0)
self.assertTrue(X[0] == 0.5)
self.assertListEqual(pgamma[:2].tolist(), [1,0])
self.assertEqual(gamma, pgamma)
self.assertEqual(gamma + pgamma, gamma)
self.assertEqual(pgamma + X, X)
self.assertNotEqual(gamma, X)
self.assertEqual(X.norm, (gamma + X).norm)
self.assertEqual(X.norm, (gamma + X).norm)
self.assertEqual(X.norm, np.sqrt(np.sum(X.cart_coords**2)))
self.assertTrue(hash(gamma) == hash(pgamma))
if hash(K) != hash(X):
self.assertTrue(K != X)
# test ob_border
self.assertFalse(gamma.on_border)
self.assertTrue(X.on_border)
self.assertFalse(K.on_border)
def pwwtows_inplace(self):
"""Wrap the kpoint to the interval ]-1/2,1/2] and update pwwave accordingly."""
kpoint = Kpoint(self.gsphere.kpoint, self.gsphere.gprimd)
wkpt = kpoint.wrap_to_ws()
if np.allclose(wkpt.rcoord, kpoint.rcoord):
return
#@David FIXME this is wrong
gvector = np.array(kpoint.rcoord - wkpt.rcoord, np.int)
self.gsphere.gvecs = self.gsphere.gvecs + gvector
self.gsphere.kpoint = wkpt.rcoord
def test_askpoints(self):
"""Test askpoints."""
lattice = self.lattice
kpts = as_kpoints([1, 2, 3], lattice)
self.serialize_with_pickle(kpts, protocols=[-1])
newkpts = as_kpoints(kpts, lattice)
self.assertTrue(kpts is newkpts)
kpts = as_kpoints([1, 2, 3, 4, 5, 6], lattice)
self.assertTrue(len(kpts) == 2)
self.assertTrue(kpts[0] == Kpoint([1, 2, 3], lattice))
self.assertTrue(kpts[1] == Kpoint([4, 5, 6], lattice))
def __init__(self, ecut, lattice, kpoint, gvecs, istwfk=1):
"""
Args:
ecut:
Cutoff energy in Hartree.
lattice:
Reciprocal lattice.
kpoint:
Reduced coordinates of the k-point.
gvecs:
Array with the reduced coordinates of the G-vectors.
istwfk:
Storage option (time-reversal symmetry, see abinit variable)
"""
self.ecut = ecut
self.lattice = lattice
self.kpoint = Kpoint.askpoint(kpoint, lattice)
self._gvecs = np.reshape(np.array(gvecs), (-1, 3))
self.npw = self.gvecs.shape[0]
self.istwfk = istwfk
if istwfk != 1:
raise NotImplementedError("istwfk %d is not implemented" % self.istwfk)
def _find_iqpt_qpoint(self, qpoint):
if duck.is_intlike(qpoint):
iq = qpoint
qpoint = self.qpoints[iq]
else:
qpoint = Kpoint.as_kpoint(qpoint, self.structure.reciprocal_lattice)
iq = self.qpoints.index(qpoint)
return iq, qpoint
def from_dict(cls, d):
ovl_from_dict = cls(d['_wfk_files'],
rspace_translations=d['_rspace_trans']['real'])
for k, v in d.items():
if k == '_wfk_files' or k == '_rspace_trans':
continue
kpt0 = Kpoint(v['kpt0']['frac_coords'],
pmg.Lattice.from_dict(
v['kpt0']['reciprocal_lattice']),
weight=v['kpt0']['weight'],
name=v['kpt0']['name'])
kpt1 = Kpoint(v['kpt1']['frac_coords'],
pmg.Lattice.from_dict(
v['kpt1']['reciprocal_lattice']),
weight=v['kpt1']['weight'],
name=v['kpt1']['name'])
ovl_from_dict[((v['wfk0'], kpt0), (v['wfk1'], kpt1))] = np.array(
v['val']['real'], dtype=complex) + 1.j * np.array(
v['val']['imag'], dtype=complex)
return ovl_from_dict
def __init__(self, qpoint, freq, displ_cart, structure):
"""
Args:
qpoint: qpoint in reduced coordinates.
freq: Phonon frequency in eV.
displ: Displacement (Cartesian coordinates, Angstrom)
structure: :class:`Structure` object.
"""
self.qpoint = Kpoint.as_kpoint(qpoint, structure.reciprocal_lattice)
self.freq = freq
self.displ_cart = displ_cart
self.structure = structure
def __init__(self, qpoint, freq, displ_cart, structure):
"""
Args:
qpoint: qpoint in reduced coordinates.
freq: Phonon frequency in eV.
displ: Displacement (Cartesian coordinates, Angstrom)
structure: :class:`Structure` object.
"""
self.qpoint = Kpoint.as_kpoint(qpoint, structure.reciprocal_lattice)
self.freq = freq
self.displ_cart = displ_cart
self.structure = structure
def pww_translation_inplace(self, gvector, rprimd=None):
"""Translates the pwwave from 1 kpoint by one gvector."""
if rprimd is None:
rprimd = self.structure.lattice.matrix
# self.gsphere.kpoint = self.gsphere.kpoint + gvector
self.gsphere.kpoint = self.gsphere.kpoint + Kpoint(
gvector, self.gsphere.kpoint.lattice)
# self.gsphere.gvecs = self.gsphere.gvecs + gvector
self.gsphere._gvecs = self.gsphere.gvecs - gvector
# fft_ndivs = (self.mesh.shape[0] + 2, self.mesh.shape[1] + 2, self.mesh.shape[2] + 2)
# newmesh = Mesh3D(fft_ndivs, rprimd, pbc=True)
# self.mesh = newmesh
self.delete_ur() # ur will get recomputed correctly as needed
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1 / 2, 1 / 2, 1 / 2, 1 / 3, 1 / 3, 1 / 3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
assert klist.sum_weights() == 1
assert len(klist) == 3
for i, kpoint in enumerate(klist):
assert kpoint in klist
assert klist.count(kpoint) == 1
assert klist.find(kpoint) == i
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist:
kpoint.set_weight(1.0)
assert np.all(klist.weights == 1.0)
# Test find_closest
iclose, kclose, dist = klist.find_closest([0, 0, 0])
assert iclose == 0 and dist == 0.
iclose, kclose, dist = klist.find_closest(
Kpoint([0.001, 0.002, 0.003], klist.reciprocal_lattice))
assert iclose == 0
self.assert_almost_equal(dist, 0.001984943324127921)
frac_coords = [0, 0, 0, 1 / 2, 1 / 3, 1 / 3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
assert k in add_klist
assert add_klist.count([0, 0, 0]) == 2
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
self.assertTrue(add_klist.count([0, 0, 0]) == 1)
self.assertTrue(len(add_klist) == 4)
self.assertTrue(add_klist == add_klist.remove_duplicated())
def _make_ticks_and_labels(self, qlabels):
"""Return ticks and labels from the mapping {qred: qstring} given in qlabels."""
if qlabels is not None:
d = OrderedDict()
for qcoord, qname in qlabels.items():
# Build Kpoint instancee
qtick = Kpoint(qcoord, self.structure.reciprocal_lattice)
for q, qpoint in enumerate(self.qpoints):
if qtick == qpoint:
d[q] = qname
else:
d = self._auto_qlabels
# Return ticks, labels
return list(d.keys()), list(d.values())
def get_strings(kpoints, direction):
""" given a list of Kpoints and a direction x, y, z
return a list of strings of kpoints along the corresponding direction """
# includes the extra kpoint shifted by a gvector
# adapted from some very old code, super inefficient, should clean up
# but it's also pretty much never a bottleneck
comps, dir_comp, gvec = direction_to_vals(direction)
bz_2d_set = sorted(
set([tuple((kpt.frac_coords[i] for i in comps)) for kpt in kpoints]))
strings = []
for bz_2d_pt in bz_2d_set:
this_string = []
for kpt in kpoints:
in_this_string = (
(abs(kpt.frac_coords[comps[0]] - bz_2d_pt[0]) < 1.e-5)
and (abs(kpt.frac_coords[comps[1]] - bz_2d_pt[1]) < 1.e-5))
if in_this_string:
this_string.append(kpt)
this_string.sort(key=lambda k: k.frac_coords[dir_comp])
this_string.append(this_string[0] +
Kpoint(gvec, kpoints.reciprocal_lattice))
strings.append(this_string)
return strings
def test_kpoint_algebra(self):
"""Test k-point algebra."""
lattice = self.lattice
gamma = Kpoint([0, 0, 0], lattice)
pgamma = Kpoint([1, 0, 1], lattice)
X = Kpoint([0.5, 0, 0], lattice)
K = Kpoint([1 / 3, 1 / 3, 1 / 3], lattice)
print(X)
# TODO
#assert np.all(np.array(X) == X.frac_coords)
self.serialize_with_pickle(X, protocols=[-1])
self.assert_almost_equal(X.versor().norm, 1.0)
self.assertTrue(X[0] == 0.5)
self.assertListEqual(pgamma[:2].tolist(), [1, 0])
self.assertEqual(gamma, pgamma)
self.assertEqual(gamma + pgamma, gamma)
self.assertEqual(pgamma + X, X)
self.assertNotEqual(gamma, X)
self.assertEqual(X.norm, (gamma + X).norm)
self.assertEqual(X.norm, (gamma + X).norm)
self.assertEqual(X.norm, np.sqrt(np.sum(X.cart_coords**2)))
self.assertTrue(hash(gamma) == hash(pgamma))
if hash(K) != hash(X):
self.assertTrue(K != X)
# test on_border
self.assertFalse(gamma.on_border)
self.assertTrue(X.on_border)
self.assertFalse(K.on_border)
def test_kpoint_algebra(self):
"""Test k-point algebra."""
lattice = self.lattice
gamma = Kpoint([0, 0, 0], lattice)
pgamma = Kpoint([1, 0, 1], lattice)
X = Kpoint([0.5, 0, 0], lattice)
K = Kpoint([1 / 3, 1 / 3, 1 / 3], lattice)
repr(X)
str(X)
assert X.to_string(verbose=2)
assert gamma.is_gamma()
assert not pgamma.is_gamma()
assert pgamma.is_gamma(allow_umklapp=True)
assert not X.is_gamma()
# TODO
#assert np.all(np.array(X) == X.frac_coords)
self.serialize_with_pickle(X, protocols=[-1])
self.assert_almost_equal(X.versor().norm, 1.0)
other_gamma = Kpoint.gamma(lattice, weight=1)
assert other_gamma == [0, 0, 0]
assert other_gamma == gamma
assert gamma.versor() == gamma
X_outside = Kpoint([1.5, 0, 0], lattice)
assert X_outside.wrap_to_ws() == X
assert X_outside.wrap_to_ws() == [0.5, 0, 0]
X_outside = Kpoint([0.7, 0, 0], lattice)
assert X_outside.wrap_to_bz() == [-0.3, 0, 0]
assert X[0] == 0.5
self.assert_equal(pgamma[:2].tolist(), [1, 0])
assert gamma == pgamma
assert gamma + pgamma == gamma
assert pgamma + X == X
assert gamma != X
# TODO
#assert gamma != 0
assert X.norm == (gamma + X).norm
assert X.norm == (gamma + X).norm
assert X.norm == np.sqrt(np.sum(X.cart_coords**2))
# TODO
#assert X != 0.5
assert hash(gamma) == hash(pgamma)
if hash(K) != hash(X):
assert K != X
# test on_border
assert not gamma.on_border
assert X.on_border
assert not K.on_border
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1 / 2, 1 / 2, 1 / 2, 1 / 3, 1 / 3, 1 / 3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
repr(klist)
str(klist)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
self.assert_equal(klist.frac_coords.flatten(), frac_coords)
self.assert_equal(klist.get_cart_coords(),
np.reshape([k.cart_coords for k in klist], (-1, 3)))
assert klist.sum_weights() == 1
assert len(klist) == 3
for i, kpoint in enumerate(klist):
assert kpoint in klist
assert klist.count(kpoint) == 1
assert klist.find(kpoint) == i
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist:
kpoint.set_weight(1.0)
assert np.all(klist.weights == 1.0)
# Test find_closest
iclose, kclose, dist = klist.find_closest([0, 0, 0])
assert iclose == 0 and dist == 0.
iclose, kclose, dist = klist.find_closest(
Kpoint([0.001, 0.002, 0.003], klist.reciprocal_lattice))
assert iclose == 0
self.assert_almost_equal(dist, 0.001984943324127921)
# Compute mapping k_index --> (k + q)_index, g0
k2kqg = klist.get_k2kqg_map((0, 0, 0))
assert all(ikq == ik for ik, (ikq, g0) in k2kqg.items())
k2kqg = klist.get_k2kqg_map((1 / 2, 1 / 2, 1 / 2))
assert len(k2kqg) == 2
assert k2kqg[0][0] == 1 and np.all(k2kqg[0][1] == 0)
assert k2kqg[1][0] == 0 and np.all(k2kqg[1][1] == 1)
frac_coords = [0, 0, 0, 1 / 2, 1 / 3, 1 / 3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
assert k in add_klist
assert add_klist.count([0, 0, 0]) == 2
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
assert add_klist.count([0, 0, 0]) == 1
assert len(add_klist) == 4
assert add_klist == add_klist.remove_duplicated()
def test_kpoint_algebra(self):
"""Test k-point algebra."""
lattice = self.lattice
gamma = Kpoint([0, 0, 0], lattice)
pgamma = Kpoint([1, 0, 1], lattice)
X = Kpoint([0.5, 0, 0], lattice)
K = Kpoint([1/3, 1/3, 1/3], lattice)
repr(X); str(X)
assert X.to_string(verbose=2)
assert gamma.is_gamma()
assert not pgamma.is_gamma()
assert pgamma.is_gamma(allow_umklapp=True)
assert not X.is_gamma()
# TODO
#assert np.all(np.array(X) == X.frac_coords)
self.serialize_with_pickle(X, protocols=[-1])
self.assert_almost_equal(X.versor().norm, 1.0)
other_gamma = Kpoint.gamma(lattice, weight=1)
assert other_gamma == [0, 0, 0]
assert other_gamma == gamma
assert gamma.versor() == gamma
X_outside = Kpoint([1.5, 0, 0], lattice)
assert X_outside.wrap_to_ws() == X
assert X_outside.wrap_to_ws() == [0.5, 0, 0]
X_outside = Kpoint([0.7, 0, 0], lattice)
assert X_outside.wrap_to_bz() == [-0.3, 0, 0]
assert X[0] == 0.5
self.assert_equal(pgamma[:2].tolist(), [1,0])
assert gamma == pgamma
assert gamma + pgamma == gamma
assert pgamma + X == X
assert gamma != X
# TODO
#assert gamma != 0
assert X.norm == (gamma + X).norm
assert X.norm == (gamma + X).norm
assert X.norm == np.sqrt(np.sum(X.cart_coords**2))
# TODO
#assert X != 0.5
assert hash(gamma) == hash(pgamma)
if hash(K) != hash(X):
assert K != X
# test on_border
assert not gamma.on_border
assert X.on_border
assert not K.on_border
def qpoint(self):
"""Q-point object."""
return Kpoint(self.reader.read_value('qpoint'), self.structure.reciprocal_lattice)
def plot_gkq2_qpath(self, band_kq, band_k, kpoint=0, with_glr=False, qdamp=None, nu_list=None, # spherical_average=False,
ax=None, fontsize=8, eph_wtol=EPH_WTOL, **kwargs):
r"""
Plot the magnitude of the electron-phonon matrix elements <k+q, band_kq| Delta_{q\nu} V |k, band_k>
for a given set of (band_kq, band, k) as a function of the q-point.
Args:
band_ks: Band index of the k+q states (starts at 0)
band_k: Band index of the k state (starts at 0)
kpoint: |Kpoint| object or index.
with_glr: True to plot the long-range component estimated from Verdi's model.
qdamp:
nu_list: List of phonons modes to be selected (starts at 0). None to select all modes.
ax: |matplotlib-Axes| or None if a new figure should be created.
fontsize: Label and title fontsize.
Return: |matplotlib-Figure|
"""
if duck.is_intlike(kpoint):
ik = kpoint
kpoint = self.kpoints[ik]
else:
kpoint = Kpoint.as_kpoint(kpoint, self.abifiles[0].structure.reciprocal_lattice)
ik = self.kpoints.index(kpoint)
# Assume abifiles are already ordered according to q-path.
xs = list(range(len(self.abifiles)))
natom3 = len(self.abifiles[0].structure) * 3
nsppol = self.abifiles[0].nsppol
nqpt = len(self.abifiles)
gkq_snuq = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
if with_glr: gkq_lr = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
# TODO: Should take into account possible degeneracies in k and kq...
xticks, xlabels = [], []
for iq, abifile in enumerate(self.abifiles):
qpoint = abifile.qpoint
#d3q_fact = one if not spherical_average else np.sqrt(4 * np.pi) * qpoint.norm
name = qpoint.name if qpoint.name is not None else abifile.structure.findname_in_hsym_stars(qpoint)
if qpoint.name is not None:
xticks.append(iq)
xlabels.append(name)
phfreqs_ha, phdispl_red = abifile.phfreqs_ha, abifile.phdispl_red
ncvar = abifile.reader.read_variable("gkq")
for spin in range(nsppol):
gkq_atm = ncvar[spin, ik, :, band_k, band_kq]
gkq_atm = gkq_atm[:, 0] + 1j * gkq_atm[:, 1]
# Transform the gkk matrix elements from (atom, red_direction) basis to phonon-mode basis.
gkq_snuq[spin, :, iq] = 0.0
for nu in range(natom3):
if phfreqs_ha[nu] < eph_wtol: continue
gkq_snuq[spin, nu, iq] = np.dot(phdispl_red[nu], gkq_atm) / np.sqrt(2.0 * phfreqs_ha[nu])
if with_glr:
# Compute long range part with (simplified) generalized Frohlich model.
gkq_lr[spin, :, iq] = glr_frohlich(qpoint, abifile.becs_cart, abifile.epsinf_cart,
abifile.phdispl_cart_bohr, phfreqs_ha, abifile.structure, qdamp=qdamp)
ax, fig, plt = get_ax_fig_plt(ax=ax)
nu_list = list(range(natom3)) if nu_list is None else list(nu_list)
for spin in range(nsppol):
for nu in nu_list:
ys = np.abs(gkq_snuq[spin, nu]) * abu.Ha_meV
pre_label = kwargs.pop("pre_label",r"$g_{\bf q}$")
if nsppol == 1: label = r"%s $\nu$: %s" % (pre_label, nu)
if nsppol == 2: label = r"%s $\nu$: %s, spin: %s" % (pre_label, nu, spin)
ax.plot(xs, ys, linestyle="--", label=label)
if with_glr:
# Plot model with G = 0 and delta_nn'
ys = np.abs(gkq_lr[spin, nu]) * abu.Ha_meV
label = r"$g_{\bf q}^{\mathrm{lr0}}$ $\nu$: %s" % nu
ax.plot(xs, ys, linestyle="", marker="o", label=label)
ax.grid(True)
ax.set_xlabel("Wave Vector")
ax.set_ylabel(r"$|g_{\bf q}|$ (meV)")
if xticks:
ax.set_xticks(xticks, minor=False)
ax.set_xticklabels(xlabels, fontdict=None, minor=False, size=kwargs.pop("klabel_size", "large"))
ax.legend(loc="best", fontsize=fontsize, shadow=True)
title = r"$band_{{\bf k} + {\bf q}: %s, band_{\bf{k}}: %s, kpoint: %s" % (band_kq, band_k, repr(kpoint))
ax.set_title(title, fontsize=fontsize)
return fig
def main():
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(get_epilog())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = get_parser(with_epilog=True)
# Parse command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
if not options.command:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
if options.verbose > 2:
print(options)
if options.command == "spglib":
structure = abilab.Structure.from_file(options.filepath)
print(
structure.spget_summary(symprec=options.symprec,
angle_tolerance=options.angle_tolerance,
verbose=options.verbose))
#remove_equivalent_atoms(structure)
elif options.command == "abispg":
structure = abilab.Structure.from_file(options.filepath)
spgrp = structure.abi_spacegroup
if spgrp is not None:
print(structure.spget_summary(verbose=options.verbose))
else:
# Here we compare Abinit wrt spglib. If spgrp is None, we create a temporary
# task to run the code in dry-run mode.
print("FILE does not contain Abinit symmetry operations.")
print(
"Calling Abinit in --dry-run mode with chkprim = 0 to get space group."
)
from abipy.data.hgh_pseudos import HGH_TABLE
gsinp = factories.gs_input(structure,
HGH_TABLE,
spin_mode="unpolarized")
gsinp["chkprim"] = 0
abistructure = gsinp.abiget_spacegroup(tolsym=options.tolsym)
print(abistructure.spget_summary(verbose=options.verbose))
diff_structures(
[structure, abistructure],
mode=options.diff_mode,
headers=["Input structure", "After Abinit symmetrization"],
fmt="abivars")
# Save file.
save_structure(abistructure, options)
elif options.command == "convert":
fmt = options.format
if fmt == "cif" and options.filepath.endswith(".cif"): fmt = "abivars"
print(abilab.Structure.from_file(options.filepath).convert(fmt=fmt))
elif options.command == "supercell":
structure = abilab.Structure.from_file(options.filepath)
options.scaling_matrix = np.array(options.scaling_matrix)
if len(options.scaling_matrix) == 9:
options.scaling_matrix.shape = (3, 3)
if options.verbose:
print("scaling matrix: ", options.scaling_matrix)
supcell = structure * options.scaling_matrix
#supcell = structure.make_supercell(scaling_matrix, to_unit_cell=True)
print(supcell.convert(fmt=options.format))
elif options.command == "abisanitize":
print("\nCalling abi_sanitize to get a new structure in which:")
print(" * Structure is refined.")
print(" * Reduced to primitive settings.")
print(
" * Lattice vectors are exchanged if the triple product is negative\n"
)
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.abi_sanitize(
symprec=options.symprec,
angle_tolerance=options.angle_tolerance,
primitive=not options.no_primitive,
primitive_standard=options.primitive_standard)
index = [options.filepath, "abisanitized"]
dfs = abilab.dataframes_from_structures([structure, sanitized],
index=index,
with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
abilab.print_dataframe(
dfs.coords,
title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
#print(sanitized.convert(fmt="cif"))
else:
#print("\nDifference between structures:")
if len(structure) == len(sanitized):
table = []
for line1, line2 in zip(
str(structure).splitlines(),
str(sanitized).splitlines()):
table.append([line1, line2])
print(
str(
tabulate(table,
headers=["Initial structure",
"Abisanitized"])))
else:
print("\nInitial structure:")
print(structure)
print("\nabisanitized structure:")
print(sanitized)
# Save file.
save_structure(sanitized, options)
elif options.command == "irefine":
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.copy()
symprec, angle_tolerance = options.symprec, options.angle_tolerance
print(
"Calling abi_sanitize with increasing tolerances to reach target space group:",
options.target_spgnum)
print("Using symprec_step: ", options.symprec_step,
", angle_tolerance_step:", options.angle_tolerance_step,
"ntrial", options.ntrial)
itrial = 0
while itrial < options.ntrial:
print(">>> Trying with symprec: %s, angle_tolerance: %s" %
(symprec, angle_tolerance))
sanitized = sanitized.abi_sanitize(
symprec=symprec,
angle_tolerance=angle_tolerance,
primitive=not options.no_primitive,
primitive_standard=options.primitive_standard)
spg_symb, spg_num = sanitized.get_space_group_info(
symprec=symprec, angle_tolerance=angle_tolerance)
print(">>> Space-group number:", spg_symb, ", symbol:", spg_num,
"for trial:", itrial)
if spg_num == options.target_spgnum:
print(2 * "\n", "# Final structure with space group number:",
spg_symb, ", symbol:", spg_num, 2 * "\n")
print(sanitized.convert(fmt="cif"))
break
# Increment counter and tols.
itrial += 1
symprec += options.symprec_step
angle_tolerance += options.angle_tolerance_step
else:
print("Cannot find space group number:", options.target_spgnum,
"after", options.ntrial, "iterations")
return 1
# Save file.
#save_structure(sanitized, options)
elif options.command == "conventional":
print(
"\nCalling get_conventional_standard_structure to get conventional structure:"
)
print(
"The standards are defined in Setyawan, W., & Curtarolo, S. (2010). "
)
print(
"High-throughput electronic band structure calculations: Challenges and tools. "
)
print(
"Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010\n"
)
structure = abilab.Structure.from_file(options.filepath)
conv = structure.get_conventional_standard_structure(
international_monoclinic=True,
symprec=options.symprec,
angle_tolerance=options.angle_tolerance)
index = [options.filepath, "conventional"]
dfs = abilab.dataframes_from_structures([structure, conv],
index=index,
with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
if options.verbose:
abilab.print_dataframe(
dfs.coords,
title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
else:
#print("\nDifference between structures:")
if len(structure) == len(conv):
table = []
for line1, line2 in zip(
str(structure).splitlines(),
str(conv).splitlines()):
table.append([line1, line2])
print(
str(
tabulate(table,
headers=["Initial structure",
"Conventional"])))
else:
print("\nInitial structure:\n", structure)
print("\nConventional structure:\n", conv)
# Save file.
save_structure(conv, options)
elif options.command == "neighbors":
abilab.Structure.from_file(
options.filepath).print_neighbors(radius=options.radius)
elif options.command == "interpolate":
initial_structure = abilab.Structure.from_file(options.filepaths[0])
end_structure = abilab.Structure.from_file(options.filepaths[1])
structures = initial_structure.interpolate(
end_structure,
nimages=options.nimages,
interpolate_lattices=False,
pbc=True,
autosort_tol=options.autosort_tol)
structures = list(map(abilab.Structure.as_structure, structures))
for i, s in enumerate(structures):
print(marquee("Structure #%d" % i, mark="="))
print(s.convert(fmt=options.format))
print(" ")
elif options.command == "xrd":
structure = abilab.Structure.from_file(options.filepath)
two_theta_range = tuple(float(t) for t in options.two_theta_range)
structure.plot_xrd(wavelength=options.wavelength,
two_theta_range=two_theta_range,
symprec=options.symprec,
annotate_peaks=not options.no_annotate_peaks)
elif options.command == "oxistate":
print(
abilab.Structure.from_file(
options.filepath).get_oxi_state_decorated())
elif options.command == "ipython":
structure = abilab.Structure.from_file(options.filepath)
print(
"Invoking Ipython, `structure` object will be available in the Ipython terminal"
)
import IPython
IPython.start_ipython(argv=[], user_ns={"structure": structure})
elif options.command == "notebook":
structure = abilab.Structure.from_file(options.filepath)
structure.make_and_open_notebook(nbpath=None,
foreground=options.foreground)
elif options.command == "visualize":
structure = abilab.Structure.from_file(options.filepath)
print(structure)
print("Visualizing structure with:", options.appname)
structure.visualize(appname=options.appname)
elif options.command == "kpath":
structure = abilab.Structure.from_file(options.filepath)
print("# Abinit Structure")
print(structure.abi_string)
print("\n# K-path in reduced coordinates:")
print("# tolwfr 1e-20 iscf -2 getden ??")
print(" ndivsm 10")
print(" kptopt", -(len(structure.hsym_kpoints) - 1))
print(" kptbounds")
for k in structure.hsym_kpoints:
print(" %+.5f %+.5f %+.5f" % tuple(k.frac_coords), "#",
k.name)
elif options.command == "bz":
abilab.Structure.from_file(options.filepath).plot_bz()
elif options.command == "ngkpt":
d = abilab.Structure.from_file(options.filepath).calc_ksampling(
options.nksmall)
print("ngkpt %d %d %d" % (d.ngkpt[0], d.ngkpt[1], d.ngkpt[2]))
print("nshiftk ", len(d.shiftk), "\nshiftk")
for s in d.shiftk:
print(" %s %s %s" % (s[0], s[1], s[2]))
elif options.command == "ktables":
structure = abilab.Structure.from_file(options.filepath)
k = Ktables(structure, options.mesh, options.is_shift,
not options.no_time_reversal)
print(k)
print("")
print(
"NB: These results are obtained by calling spglib with the structure read from file."
)
print(
"The k-points might differ from the ones expected by Abinit, especially if the space groups differ."
)
if not options.verbose:
print("\nUse -v to obtain the BZ --> IBZ mapping.")
else:
print()
k.print_bz2ibz()
elif options.command == "abikmesh":
structure = abilab.Structure.from_file(options.filepath)
from abipy.data.hgh_pseudos import HGH_TABLE
gsinp = factories.gs_input(structure,
HGH_TABLE,
spin_mode="unpolarized",
kppa=options.kppa)
if options.kppa is not None:
print("Calling Abinit to compute the IBZ with kppa:", options.kppa,
"and shiftk:", options.shiftk)
options.ngkpt = None
else:
print("Calling Abinit to compute the IBZ with ngkpt:",
options.ngkpt, "and shiftk", options.shiftk)
ibz = gsinp.abiget_ibz(ngkpt=options.ngkpt,
shiftk=options.shiftk,
kptopt=options.kptopt)
if options.verbose:
print(gsinp)
print("Found %d points in the IBZ:" % len(ibz.points))
for i, (k, w) in enumerate(zip(ibz.points, ibz.weights)):
print("%6d) [%+.3f, %+.3f, %+.3f] weight=%.3f" %
(i, k[0], k[1], k[2], w))
#elif options.command == "kmesh_jhu":
# structure = abilab.Structure.from_file(options.filepath)
# ksampling = structure.ksampling_from_jhudb(kppra=1000)
# #print(ksampling)
elif options.command == "lgk":
structure = abilab.Structure.from_file(options.filepath)
spgrp = structure.abi_spacegroup
if spgrp is None:
cprint("Your file does not contain Abinit symmetry operations.",
"yellow")
cprint(
"Will call spglib to obtain the space group (assuming time-reversal: %s)"
% (not options.no_time_reversal), "yellow")
spgrp = AbinitSpaceGroup.from_structure(
structure,
has_timerev=not options.no_time_reversal,
symprec=options.symprec,
angle_tolerance=options.angle_tolerance)
print()
print(marquee("Structure", mark="="))
print(structure.spget_summary(verbose=options.verbose))
print("\n")
print(marquee("Little Group", mark="="))
ltk = spgrp.find_little_group(kpoint=options.kpoint)
print(ltk.to_string(verbose=options.verbose))
elif options.command == "kstar":
structure = abilab.Structure.from_file(options.filepath)
# TODO
#kstar = structure.get_star_kpoint(options.kpoint, has_timerev=not options.no_time_reversal)
# Call spglib to get spacegroup if Abinit spacegroup is not available.
if structure.abi_spacegroup is None:
structure.spgset_abi_spacegroup(
has_timerev=not options.no_time_reversal)
kpoint = Kpoint(options.kpoint, structure.reciprocal_lattice)
kstar = kpoint.compute_star(structure.abi_spacegroup, wrap_tows=True)
print("Found %s points in the star of %s\n" %
(len(kstar), repr(kpoint)))
for k in kstar:
print(4 * " ", repr(k))
elif options.command == "mp_id":
# Get the Structure corresponding to material_id.
structure = abilab.Structure.from_mpid(options.mpid,
final=True,
api_key=options.mapi_key,
endpoint=options.endpoint)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "mp_match":
mp = abilab.mp_match_structure(options.filepath)
if not mp.structures:
cprint("No structure found in database", "yellow")
return 1
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_search":
mp = abilab.mp_search(options.chemsys_formula_id)
if not mp.structures:
cprint("No structure found in Materials Project database",
"yellow")
return 1
if options.select_spgnum:
mp = mp.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_pd":
if os.path.exists(options.file_or_elements):
structure = abilab.Structure.from_file(options.file_or_elements)
elements = structure.symbol_set
else:
elements = options.file_or_elements.split("-")
if options.verbose > 1:
print("Building phase-diagram for elements:", elements)
with abilab.restapi.get_mprester(api_key=options.mapi_key,
endpoint=options.endpoint) as rest:
pdr = rest.get_phasediagram_results(elements)
pdr.print_dataframes(verbose=options.verbose)
pdr.plot(show_unstable=options.show_unstable)
elif options.command == "cod_search":
cod = abilab.cod_search(options.formula, primitive=options.primitive)
if not cod.structures:
cprint("No structure found in COD database", "yellow")
return 1
if options.select_spgnum:
cod = cod.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return cod.make_and_open_notebook(foreground=options.foreground)
else:
cod.print_results(fmt=options.format, verbose=options.verbose)
elif options.command == "cod_id":
# Get the Structure from COD
structure = abilab.Structure.from_cod_id(options.cod_identifier,
primitive=options.primitive)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "animate":
filepath = options.filepath
if any(filepath.endswith(ext) for ext in ("HIST", "HIST.nc")):
with abilab.abiopen(filepath) as hist:
structures = hist.structures
elif "XDATCAR" in filepath:
structures = Xdatcar(filepath).structures
if not structures:
raise RuntimeError(
"Your Xdatcar contains only one structure. Due to a bug "
"in the pymatgen routine, your structures won't be parsed correctly"
"Solution: Add another structure at the end of the file.")
else:
raise ValueError("Don't know how to handle file %s" % filepath)
xsf_write_structure(sys.stdout, structures)
else:
raise ValueError("Unsupported command: %s" % options.command)
return 0
def test_kpath_api(self):
"""Testing Kpath API."""
structure = abilab.Structure.as_structure(abidata.cif_file("si.cif"))
knames = ["G", "X", "L", "G"]
kpath = Kpath.from_names(structure, knames, line_density=5)
repr(kpath)
str(kpath)
assert kpath.to_string(verbose=2, title="Kpath")
assert not kpath.is_ibz and kpath.is_path
assert kpath[0].is_gamma and kpath[-1].is_gamma
#assert len(kpath.ds) == len(self) - 1
#assert kpath.ksampling.kptopt == 1
#self.assert_equal(kpath.ksampling.mpdivs, [4, 4, 4])
assert Kpoint.from_name_and_structure("Gamma", structure) == kpath[0]
assert len(kpath.ds) == len(kpath) - 1
assert len(kpath.versors) == len(kpath) - 1
assert len(kpath.lines) == len(knames) - 1
self.assert_almost_equal(kpath.frac_bounds,
structure.get_kcoords_from_names(knames))
self.assert_almost_equal(
kpath.cart_bounds,
structure.get_kcoords_from_names(knames, cart_coords=True))
r = kpath.find_points_along_path(kpath.get_cart_coords())
assert len(r.ikfound) == len(kpath)
self.assert_equal(
r.ikfound,
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 0])
#kpath = IrredZone.from_kppa(structure, kppa=1000, shiftk=[0.5, 0.5, 0.5], kptopt=1, verbose=1)
#assert not kpath.is_ibz and kpath.is_path
#assert len(kpath) == 60
#self.assert_equal(kpath.ksampling.mpdivs, [8, 8, 8])
segments = build_segments(
k0_list=(0, 0, 0),
npts=1,
step=0.01,
red_dirs=(1, 0, 0),
reciprocal_lattice=structure.reciprocal_lattice)
assert len(segments) == 1
assert np.all(segments[0] == (0, 0, 0))
step, npts = 0.1, 5
red_dir = np.array((1, 1, 0))
segments = build_segments(
k0_list=(0, 0, 0, 0.5, 0, 0),
npts=npts,
step=step,
red_dirs=red_dir,
reciprocal_lattice=structure.reciprocal_lattice)
#print("segments:\n", segments)
# (nk0_list, len(red_dirs) * npts, 3)
assert segments.shape == (2, npts, 3)
self.assert_almost_equal(segments[0, 2], (0, 0, 0))
self.assert_almost_equal(segments[1, 2], (0.5, 0.0, 0))
def r2c(vec):
return structure.reciprocal_lattice.get_cartesian_coords(vec)
cart_vers = r2c(red_dir)
cart_vers /= np.linalg.norm(cart_vers)
self.assert_almost_equal(r2c(segments[1, 1] - segments[1, 0]),
step * cart_vers)
self.assert_almost_equal(r2c(segments[1, 3] - segments[1, 2]),
step * cart_vers)
def plot(self, qpoint=None, spin=None, kpoints=None, color_map=None, **kwargs):
"""
Plot the dipole matrix elements.
Args:
qpoint:
The qpoint for the optical limit.
if qpoint is None, we plot |<k|r|k>| else |<k|q.r|k>|
spin:
spin index. None if all spins are wanted
kpoints:
List of Kpoint objects, None if all k-points are wanted.
============== ==============================================================
kwargs Meaning
============== ==============================================================
title Title of the plot (Default: None).
show True to show the figure (Default).
savefig: 'abc.png' or 'abc.eps'* to save the figure to a file.
colormap matplotlib colormap, see link below.
============== ==============================================================
Returns:
matplotlib figure.
.. see:
http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html
"""
title = kwargs.pop("title", None)
show = kwargs.pop("show", True)
savefig = kwargs.pop("savefig", None)
color_map = kwargs.pop("color_map", None)
if qpoint is not None:
# Will compute scalar product with q
qpoint = Kpoint.askpoint(qpoint, self.structure.reciprocal_lattice).versor()
else:
# Will plot |<psi|r|psi>|.
qpoint = Kpoint((1, 1, 1), self.structure.reciprocal_lattice)
if spin in None:
spins = range(self.nsppol)
else:
spins = [spin]
if kpoints is None:
kpoints = self.ibz
# Extract the matrix elements for the plot.
from abipy.tools.plotting_utils import ArrayPlotter
plotter = ArrayPlotter()
for spin in spins:
for kpoint in kpoints:
ik = self.kpoint_index(kpoint)
rme = self.dipme_scvk[spin, ik, :, :, :]
#qrme = qpoint * rme
label = "qpoint %s, spin %s, kpoint = %s" % (qpoint, spin, kpoint)
plotter.add_array(label, rme)
# Plot matrix elements and return matplotlib figure.
return plotter.plot(title=title, color_map=color_map, show=show, savefig=savefig, **kwargs)
def main():
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(get_epilog())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = get_parser(with_epilog=True)
# Parse command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
if not options.command:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
if options.verbose > 2:
print(options)
if options.command == "spglib":
structure = abilab.Structure.from_file(options.filepath)
print(structure.spget_summary(symprec=options.symprec, angle_tolerance=options.angle_tolerance,
verbose=options.verbose))
#remove_equivalent_atoms(structure)
elif options.command == "abispg":
structure = abilab.Structure.from_file(options.filepath)
check_ordered_structure(structure)
spgrp = structure.abi_spacegroup
if spgrp is not None:
print(structure.spget_summary(verbose=options.verbose))
else:
# Here we compare Abinit wrt spglib. If spgrp is None, we create a temporary
# task to run the code in dry-run mode.
print("FILE does not contain Abinit symmetry operations.")
print("Calling Abinit in --dry-run mode with chkprim = 0 to get space group.")
from abipy.data.hgh_pseudos import HGH_TABLE
gsinp = factories.gs_input(structure, HGH_TABLE, spin_mode="unpolarized")
gsinp["chkprim"] = 0
abistructure = gsinp.abiget_spacegroup(tolsym=options.tolsym)
print(abistructure.spget_summary(verbose=options.verbose))
diff_structures([structure, abistructure], mode=options.diff_mode,
headers=["Input structure", "After Abinit symmetrization"], fmt="abivars")
# Save file.
save_structure(abistructure, options)
elif options.command == "convert":
fmt = options.format
if fmt == "cif" and options.filepath.endswith(".cif"): fmt = "abivars"
print(abilab.Structure.from_file(options.filepath).convert(fmt=fmt))
elif options.command == "supercell":
structure = abilab.Structure.from_file(options.filepath)
options.scaling_matrix = np.array(options.scaling_matrix)
if len(options.scaling_matrix) == 9:
options.scaling_matrix.shape = (3, 3)
if options.verbose:
print("scaling matrix: ", options.scaling_matrix)
supcell = structure * options.scaling_matrix
#supcell = structure.make_supercell(scaling_matrix, to_unit_cell=True)
print(supcell.convert(fmt=options.format))
elif options.command == "abisanitize":
print("\nCalling abi_sanitize to get a new structure in which:")
print(" * Structure is refined.")
print(" * Reduced to primitive settings.")
print(" * Lattice vectors are exchanged if the triple product is negative\n")
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.abi_sanitize(symprec=options.symprec, angle_tolerance=options.angle_tolerance,
primitive=not options.no_primitive, primitive_standard=options.primitive_standard)
index = [options.filepath, "abisanitized"]
dfs = abilab.dataframes_from_structures([structure, sanitized], index=index, with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
#print(sanitized.convert(fmt="cif"))
else:
#print("\nDifference between structures:")
if len(structure) == len(sanitized):
table = []
for line1, line2 in zip(str(structure).splitlines(), str(sanitized).splitlines()):
table.append([line1, line2])
print(str(tabulate(table, headers=["Initial structure", "Abisanitized"])))
else:
print("\nInitial structure:")
print(structure)
print("\nabisanitized structure:")
print(sanitized)
# Save file.
save_structure(sanitized, options)
elif options.command == "irefine":
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.copy()
symprec, angle_tolerance = options.symprec, options.angle_tolerance
print("Calling abi_sanitize with increasing tolerances to reach target space group:", options.target_spgnum)
print("Using symprec_step: ", options.symprec_step, ", angle_tolerance_step:", options.angle_tolerance_step,
"ntrial", options.ntrial)
itrial = 0
while itrial < options.ntrial:
print(">>> Trying with symprec: %s, angle_tolerance: %s" % (symprec, angle_tolerance))
sanitized = sanitized.abi_sanitize(symprec=symprec, angle_tolerance=angle_tolerance,
primitive=not options.no_primitive, primitive_standard=options.primitive_standard)
spg_symb, spg_num = sanitized.get_space_group_info(symprec=symprec, angle_tolerance=angle_tolerance)
print(">>> Space-group number:", spg_symb, ", symbol:", spg_num, "for trial:", itrial)
if spg_num == options.target_spgnum:
print(2 * "\n", "# Final structure with space group number:", spg_symb, ", symbol:", spg_num, 2 *"\n")
print(sanitized.convert(fmt="cif"))
break
# Increment counter and tols.
itrial += 1
symprec += options.symprec_step
angle_tolerance += options.angle_tolerance_step
else:
print("Cannot find space group number:", options.target_spgnum, "after", options.ntrial, "iterations")
return 1
# Save file.
#save_structure(sanitized, options)
elif options.command == "conventional":
print("\nCalling get_conventional_standard_structure to get conventional structure:")
print("The standards are defined in Setyawan, W., & Curtarolo, S. (2010). ")
print("High-throughput electronic band structure calculations: Challenges and tools. ")
print("Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010\n")
structure = abilab.Structure.from_file(options.filepath)
conv = structure.get_conventional_standard_structure(international_monoclinic=True,
symprec=options.symprec, angle_tolerance=options.angle_tolerance)
index = [options.filepath, "conventional"]
dfs = abilab.dataframes_from_structures([structure, conv], index=index, with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
if options.verbose:
abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
else:
#print("\nDifference between structures:")
if len(structure) == len(conv):
table = []
for line1, line2 in zip(str(structure).splitlines(), str(conv).splitlines()):
table.append([line1, line2])
print(str(tabulate(table, headers=["Initial structure", "Conventional"])))
else:
print("\nInitial structure:\n", structure)
print("\nConventional structure:\n", conv)
# Save file.
save_structure(conv, options)
elif options.command == "neighbors":
abilab.Structure.from_file(options.filepath).print_neighbors(radius=options.radius)
elif options.command == "interpolate":
initial_structure = abilab.Structure.from_file(options.filepaths[0])
end_structure = abilab.Structure.from_file(options.filepaths[1])
structures = initial_structure.interpolate(end_structure, nimages=options.nimages,
interpolate_lattices=False, pbc=True,
autosort_tol=options.autosort_tol)
structures = list(map(abilab.Structure.as_structure, structures))
for i, s in enumerate(structures):
print(marquee("Structure #%d" % i, mark="="))
print(s.convert(fmt=options.format))
print(" ")
elif options.command == "xrd":
structure = abilab.Structure.from_file(options.filepath)
two_theta_range = tuple(float(t) for t in options.two_theta_range)
structure.plot_xrd(wavelength=options.wavelength, two_theta_range=two_theta_range,
symprec=options.symprec, annotate_peaks=not options.no_annotate_peaks)
elif options.command == "oxistate":
print(abilab.Structure.from_file(options.filepath).get_oxi_state_decorated())
elif options.command == "ipython":
structure = abilab.Structure.from_file(options.filepath)
print("Invoking Ipython, `structure` object will be available in the Ipython terminal")
import IPython
IPython.start_ipython(argv=[], user_ns={"structure": structure})
elif options.command == "notebook":
structure = abilab.Structure.from_file(options.filepath)
structure.make_and_open_notebook(nbpath=None, foreground=options.foreground)
elif options.command == "visualize":
structure = abilab.Structure.from_file(options.filepath)
print(structure)
print("Visualizing structure with:", options.appname)
structure.visualize(appname=options.appname)
elif options.command == "kpath":
structure = abilab.Structure.from_file(options.filepath)
print(structure.get_kpath_input_string(fmt=options.format, line_density=10))
elif options.command == "bz":
abilab.Structure.from_file(options.filepath).plot_bz()
elif options.command == "ngkpt":
d = abilab.Structure.from_file(options.filepath).calc_ksampling(options.nksmall)
print("ngkpt %d %d %d" % (d.ngkpt[0], d.ngkpt[1], d.ngkpt[2]))
print("nshiftk ", len(d.shiftk), "\nshiftk")
for s in d.shiftk:
print(" %s %s %s" % (s[0], s[1], s[2]))
elif options.command == "ktables":
structure = abilab.Structure.from_file(options.filepath)
k = Ktables(structure, options.mesh, options.is_shift, not options.no_time_reversal)
print(k)
print("")
print("NB: These results are obtained by calling spglib with the structure read from file.")
print("The k-points might differ from the ones expected by Abinit, especially if the space groups differ.")
if not options.verbose:
print("\nUse -v to obtain the BZ --> IBZ mapping.")
else:
print()
k.print_bz2ibz()
elif options.command == "abikmesh":
structure = abilab.Structure.from_file(options.filepath)
if options.kppa is None and options.ngkpt is None:
raise ValueError("Either ngkpt or kppa must be provided")
if options.kppa is not None:
print("Calling Abinit to compute the IBZ with kppa:", options.kppa, "and shiftk:", options.shiftk)
ibz = IrredZone.from_kppa(structure, options.kppa, options.shiftk,
kptopt=options.kptopt, verbose=options.verbose)
else:
print("Calling Abinit to compute the IBZ with ngkpt:", options.ngkpt, "and shiftk:", options.shiftk)
ibz = IrredZone.from_ngkpt(structure, options.ngkpt, options.shiftk,
kptopt=options.kptopt, verbose=options.verbose)
print(ibz.to_string(verbose=options.verbose))
#elif options.command == "kmesh_jhu":
# structure = abilab.Structure.from_file(options.filepath)
# ksampling = structure.ksampling_from_jhudb(kppra=1000)
# #print(ksampling)
elif options.command == "lgk":
structure = abilab.Structure.from_file(options.filepath)
spgrp = structure.abi_spacegroup
if spgrp is None:
cprint("Your file does not contain Abinit symmetry operations.", "yellow")
cprint("Will call spglib to obtain the space group (assuming time-reversal: %s)" %
(not options.no_time_reversal), "yellow")
spgrp = AbinitSpaceGroup.from_structure(structure, has_timerev=not options.no_time_reversal,
symprec=options.symprec, angle_tolerance=options.angle_tolerance)
print()
print(marquee("Structure", mark="="))
print(structure.spget_summary(verbose=options.verbose))
print("\n")
print(marquee("Little Group", mark="="))
ltk = spgrp.find_little_group(kpoint=options.kpoint)
print(ltk.to_string(verbose=options.verbose))
elif options.command == "kstar":
structure = abilab.Structure.from_file(options.filepath)
# Call spglib to get spacegroup if Abinit spacegroup is not available.
if structure.abi_spacegroup is None:
structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal)
kpoint = Kpoint(options.kpoint, structure.reciprocal_lattice)
kstar = kpoint.compute_star(structure.abi_spacegroup, wrap_tows=True)
print("Found %s points in the star of %s\n" % (len(kstar), repr(kpoint)))
for k in kstar:
print(4 * " ", repr(k))
elif options.command == "keq":
structure = abilab.Structure.from_file(options.filepath)
# Call spglib to get spacegroup if Abinit spacegroup is not available.
if structure.abi_spacegroup is None:
structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal)
k1, k2 = options.kpoints[:3], options.kpoints[3:6]
k1tab = structure.abi_spacegroup.symeq(k1, k2)
if k1tab.isym != -1:
print("\nk1:", k1, "and k2:", k2, "are symmetry equivalent k-points\n")
print("Related by the symmetry operation (reduced coords):\n", k1tab.op)
print("With umklapp vector Go = TO(k1) - k2 =", k1tab.g0)
else:
print(k1, "and", k2, "are NOT symmetry equivalent")
elif options.command == "mp_id":
# Get the Structure corresponding to material_id.
structure = abilab.Structure.from_mpid(options.mpid, final=True,
api_key=options.mapi_key, endpoint=options.endpoint)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "mp_match":
mp = abilab.mp_match_structure(options.filepath)
if not mp.structures:
cprint("No structure found in database", "yellow")
return 1
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_search":
mp = abilab.mp_search(options.chemsys_formula_id)
if not mp.structures:
cprint("No structure found in Materials Project database", "yellow")
return 1
if options.select_spgnum: mp = mp.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_pd":
if os.path.exists(options.file_or_elements):
structure = abilab.Structure.from_file(options.file_or_elements)
elements = structure.symbol_set
else:
elements = options.file_or_elements.split("-")
if options.verbose > 1: print("Building phase-diagram for elements:", elements)
with abilab.restapi.get_mprester(api_key=options.mapi_key, endpoint=options.endpoint) as rest:
pdr = rest.get_phasediagram_results(elements)
pdr.print_dataframes(verbose=options.verbose)
pdr.plot(show_unstable=options.show_unstable)
elif options.command == "cod_search":
cod = abilab.cod_search(options.formula, primitive=options.primitive)
if not cod.structures:
cprint("No structure found in COD database", "yellow")
return 1
if options.select_spgnum: cod = cod.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return cod.make_and_open_notebook(foreground=options.foreground)
else:
cod.print_results(fmt=options.format, verbose=options.verbose)
elif options.command == "cod_id":
# Get the Structure from COD
structure = abilab.Structure.from_cod_id(options.cod_identifier, primitive=options.primitive)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "animate":
filepath = options.filepath
if any(filepath.endswith(ext) for ext in ("HIST", "HIST.nc")):
with abilab.abiopen(filepath) as hist:
structures = hist.structures
elif "XDATCAR" in filepath:
structures = Xdatcar(filepath).structures
if not structures:
raise RuntimeError("Your Xdatcar contains only one structure. Due to a bug "
"in the pymatgen routine, your structures won't be parsed correctly"
"Solution: Add another structure at the end of the file.")
else:
raise ValueError("Don't know how to handle file %s" % filepath)
xsf_write_structure(sys.stdout, structures)
else:
raise ValueError("Unsupported command: %s" % options.command)
return 0
